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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

3upj

2.500 Å

X-ray

1996-03-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Gag-Pol polyprotein
ID:POL_HV2RO
AC:P04584
Organism:Human immunodeficiency virus type 2 subtype A
Reign:Viruses
TaxID:11720
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A41 %
B59 %


Ligand binding site composition:

B-Factor:8.694
Number of residues:29
Including
Standard Amino Acids: 29
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.017745.875

% Hydrophobic% Polar
47.0652.94
According to VolSite

Ligand :
3upj_1 Structure
HET Code: U03
Formula: C19H17O4
Molecular weight: 309.336 g/mol
DrugBank ID: DB08663
Buried Surface Area:52.76 %
Polar Surface area: 58.59 Å2
Number of
H-Bond Acceptors: 4
H-Bond Donors: 0
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
-1.3075718.815820.1872


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
CD3CD2LEU- 234.420Hydrophobic
OA6OD2ASP- 252.7123.57H-Bond
(Ligand Donor)
OA6OD1ASP- 253.46122.86H-Bond
(Ligand Donor)
CB6CBALA- 283.870Hydrophobic
CD4CBALA- 284.280Hydrophobic
CB4CD1ILE- 324.010Hydrophobic
CB4CG2VAL- 474.190Hydrophobic
CG3CD1ILE- 504.070Hydrophobic
CB5CD1ILE- 503.590Hydrophobic
OA2NILE- 503.04168.05H-Bond
(Protein Donor)
OA3NILE- 503.21131.27H-Bond
(Protein Donor)
CG3CG2ILE- 823.320Hydrophobic
CB6CD1ILE- 843.890Hydrophobic